Species dependence of enzyme-substrate encounter rates for triose phosphate isomerases

Abstract

Triose phosphate isomerase (TIM) is a diffusion-controlled enzyme whose rate is limited by the diffusional encounter of the negatively charged substrate glyceraldehyde 3-phosphate (GAP) with the homodimeric enzyme's active sites. Translational and orientational steering of GAP toward the active sites by the electrostatic field of chicken muscle TIM has been observed in previous Brownian dynamics (BD) simulations. Here we report simulations of the association of GAP with TIMs from four species with net charges at pH 7 varying from -12e to +12e. Computed second-order rate constants are in good agreement with experimental data. The BD simulations and computation of average Boltzmann factors of substrate-protein interaction energies show that the protein electrostatic potential enhances the rates for all the enzymes. There is much less variation in the computed rates than might be expected on the basis of the net charges. Comparison of the electrostatic potentials by means of similarity indices shows that this is due to conservation of the local electrostatic potentials around the active sites which are the primary determinants of electrostatic steering of the substrate.

Superefficient enzymes

“…Beside these structural features, other aspects contribute to the highly efficient catalysis of this enzyme, such as electrostatic steering of the substrate toward the active site. Wade et al carried out simulations of Brownian dynamics on the association of GAP with TIMs from four species with net charges at pH 7.0 between -12e and +12e [44]. Despite the wide variation in net charge, the rates of these enzymes show only modest differences.…”

Comparative Structural and Energetic Analysis of WW Domain–Peptide Interactions

“…Figure 3). The resulting total backbone RMSD values for the b-strands bA (residues 17-21), bB (residues 27-31) and bC (residues [36][37][38][39] and, in parentheses, for the whole b-sheet (residues 17-39), range between 0.39 Å (0.61 Å ) for hPIN1 and 1.31 Å (2.08 Å ) for hYAP65. These values are in the same range as the backbone RMSD for WW domains for which different experimental structures are available, which range from 0.25 Å (0.55 Å ) for 1EG4 versus 1EG3 (hDystrophin) to 0.87 Å (1.31 Å ) for 1K9R versus 1JMQ (hYAP65).…”

“…SI values are useful tools to classify and predict the functional properties and active sites of macromolecules. 16,[35][36][37][38] A matrix of pair-wise SI values was computed and converted into a distance matrix that was subjected to a clustering procedure.…”

Essential motions in a fungal lipase with bound substrate, covalently attached inhibitor and product

“…This work shows once again the limited value of static models (the singularity represented by the saddle point) and the need to consider the interplay between the dynamics and the nature of the energy surface. Likewise, it is important to consider not just side chain but also backbone flexibility and to take into account induced fit effects in order to correctly predict the docking of ligands (Wade et al, 1998b;De Benedetti et al, 1997). The benefits of dynamic analysis of enzymes are further highlighted (Keskin et al, 2000) in work showing that proteins with the same fold exhibit the same global dynamics while local differences are also observed that are connected with functional differences between the members of the family.…”